CEMPRA Documentation

Cumulative Effects Model for Prioritizing Recovery Actions (CEMPRA) Guidance Documentation.

Live Site: https://mattjbayly.github.io/CEMPRA_documentation/

Quick Start

Prerequisites

• Quarto installed
• Git

Publishing Workflow

Step 1: Edit on main branch

git checkout main
git pull origin main

# Edit your .qmd files, images, etc.

git add .
git commit -m "Your changes"
git push origin main

Step 2: Publish to gh-pages

git checkout gh-pages
git merge main
quarto render
git add docs/
git commit -m "Publish updates"
git push origin gh-pages
git checkout main

Important: You must run quarto render after merging main into gh-pages. The render must happen on the gh-pages branch.

One-Command Publish

After committing and pushing changes on main:

git checkout gh-pages && git merge main && quarto render && git add docs/ && git commit -m "Publish updates" && git push origin gh-pages && git checkout main

Branch Structure

Branch	Purpose	docs/ folder
main	Source files only	Ignored (in .gitignore)
gh-pages	Deployment	Tracked and pushed

Troubleshooting

Site not updating after push

• Did you run quarto render on the gh-pages branch after merging?
• Wait 2-5 minutes for GitHub Pages to deploy
• Check GitHub repo > Actions tab for deployment status
• Clear browser cache

Merge conflicts

1. Resolve conflicts in source files
2. Run quarto render again
3. Commit and push

Links

• R Package: https://github.com/essatech/CEMPRA
• Shiny App: https://github.com/essatech/CEMPRAShiny
• Shiny App (Live): https://essa.shinyapps.io/CEMPRAShiny/